calculateScore: Calculate the validation score for a new dataset

In shbrief/PCAGenomicSignatures: Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Calculate the validation score for a new dataset

Description

Calculate the validation score for a new dataset

Usage

calculateScore(dataset, RAVmodel, rescale.after = TRUE)

Arguments

dataset	A gene expression profile to be validated. Different classes of objects can be used including ExpressionSet, SummarizedExperiment, RangedSummarizedExperiment, or matrix. Rownames (genes) should be in symbol format. If it is a matrix, genes should be in rows and samples in columns.
RAVmodel	PCAGenomicSignatures object. A matrix of average loadings, an output from buildAvgLoading, can be directly provided.
rescale.after	Under the default (TRUE), the continuous scores are rescaled post assignment, so average loadings have the same standard deviation in different studies. If it is FALSE, the rescaling of column (= dividing by sqrt(sum(x^2) is done before score assignment.

Value

A list containing the score matrices for input datasets. Scores are assigned to each sample (row) for each cluster (column).

Examples

data(miniRAVmodel)
library(bcellViper)
data(bcellViper)
score <- calculateScore(dset, miniRAVmodel)

data(miniTCGA)
score <- calculateScore(miniTCGA, miniRAVmodel)

shbrief/PCAGenomicSignatures documentation built on May 3, 2023, 11:21 a.m.